[BioC] Building BioC 2.2 with R 2.7.0

[Robert Gentleman]

Hi Atro,
   Thanks for all your efforts in trouble shooting.  If I understand, 
the GO issue is now resolved but genefilter is still problematic.

   Could you try using gcc to compile rather than sunperf?  It looks 
like there are some header file issues that may be complicating the 
issue and it will take a few days to fix them and test properly (given a 
bunch of other constraints).

  best wishes
    Robert


Atro Tossavainen wrote:
> Here's the line that generated genefilter.so:
> 
> (I'm using Sun's Studio 11 compilers and enabled the use of the sunperf
> library while building R.)
> 
> CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -R/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib:/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib -L/opt/SUNWspro/lib/v8plus -L/opt/SUNWspro/prod/lib/v8plus -L/opt/SUNWspro/lib -L/opt/SUNWspro/prod/lib -L/usr/ccs/lib -lfui -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfsu -lsunmath -lmtsk -lm
> 
> I think all of the various -R, -L and -l parameters should have been
> reduced into "-library=sunperf" above.  It might not be an issue.
> 
> I removed the existing genefilter installation and tried building again
> simply with biocLite("genefilter"), which resulted in exactly the same
> problem.  I also tried building the .so by hand:
> 
> CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -library=sunperf
> 
> which resulted in exactly the same problem when loading via
> 
>> library(genefilter)
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Loading required package: survival
> Loading required package: splines
> Error in dyn.load(file, DLLpath = DLLpath, ...) : 
>   unable to load shared library '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so':
>   ld.so.1: /.../R/2.7.0/lib/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found
> Error: package/namespace load failed for 'genefilter'
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org